The Mystery of the Canadian Whiskey Fungus

The air outside a distillery warehouse smells like witch hazel and spices, with notes of candied fruit and vanilla—warm and tangy- mellow. It’s the aroma of fresh cookies cooling in the kitchen while a fancy cocktail party gets out of hand in the living room.

James Scott encountered that scent for the first time a decade ago in a town called Lakeshore, Ontario. Just across the river from Detroit, Lakeshore is where barrels of Canadian Club whiskey age in blocky, windowless warehouses. Scott, who had recently completed his PhD in mycology at the University of Toronto, had launched a business called Sporometrics. Run out of his apartment, it was a sort of consulting detective agency for companies that needed help dealing with weird fungal infestations. The first call he got after putting up his website was from a director of research at Hiram Walker Distillery named David Doyle.

Doyle had a problem. In the neighborhood surrounding his Lakeshore warehouses, homeowners were complaining about a mysterious black mold coating their houses. And the residents, following their noses, blamed the whiskey. Doyle wanted to know what the mold was and whether it was the company’s fault. Scott headed up to Lakeshore to take a look.

When he arrived at the warehouse, the first thing he noticed (after “the beautiful, sweet, mellow smell of aging Canadian whiskey,” he says) was the black stuff. It was everywhere—on the walls of buildings, on chain-link fences, on metal street signs, as if a battalion of Dickensian chimney sweeps had careened through town. “In the back of the property, there was an old stainless steel fermenter tank,” Scott says. “It was lying on its side, and it had this fungus growing all over it. Stainless steel!” The whole point of stainless steel is that things don’t grow on it.

Standing at a black-stained fence, Doyle explained that the distillery had been trying to solve the mystery for more than a decade. Mycologists at the University of Windsor were stumped. A team from the Scotch Whisky Association‘s Research Institute had taken samples and concluded it was just a thick layer of normal environmental fungi: Aspergillus, Exophiala, stuff like that. Ubiquitous and—maybe most important—in no way the distillery’s fault.

Scott shook his head. “David,” he said, “that’s not what it is. It’s something completely different.”

Leave fruit juice on its own for a few days or weeks and yeast—a type of fungus—will appear as if by magic. In one of nature’s great miracles, yeast eats sugar and excretes carbon dioxide and ethanol, the chemical that makes booze boozy. That’s fermentation.

If fermentation is a miracle of nature, then distillation is a miracle of science. Heat a fermented liquid and the lighter, more volatile chemical components—alcohols, ketones, esters, and so on—evaporate and separate from the heavier ones (like water). That vapor, cooled and condensed into a liquid, is a spirit. Do it to wine, you get brandy; beer, you get whiskey. Distill anything enough times and you get vodka. When it’s executed right, the process concentrates a remarkable array of aromatic and flavorful chemicals.

Photo: Caren Alpert

The basic technology of distillation—a still—consists of a tank for heating and a long tube that carries away the distillate to a receiving vessel. That simple design dates to somewhere between the first and third centuries AD, to the Alexandria lab of Maria the Jewess, one of the great Hellenistic alchemists. Maria and her colleagues were more interested in the secrets of life and the transmutation of elements than in getting wasted. They were trying to distill the “spirits” inherent in nature. Chinese apothecaries started making a potent, rough spirit as early as 670. But in the West, it wasn’t until the Middle Ages that anyone really started thinking about drinking hard alcohol; physicians in Salerno first tippled distilled wine in the mid-1100s. The technology kept improving: The famed Murano glassworks in Italy provided carefully engineered tubing and better glassware for allowing distilled vapors to cool and condense. Even Leonardo da Vinci worked on a still furnace design. By the late 1600s, most of Europe was smashed on cheap Dutch gin, French brandy, and corn spirits.

Distillation was literally a transformative technology. If you were a farmer, you could harvest all that grain or fruit and distill it down to a few easy-to-transport barrels of liquid. The product never spoiled and was worth more at market than the grain or fruit itself. The economics made a lot of sense.

By the 18th century, aging spirits in barrels for a few years had become standard practice. Exposure to oak improved the final product—coopers use heat to make casks, breaking down structural lignin, cellulose, and hemicellulose into weird, interesting sugars that dissolve into the spirit. Depending on humidity and temperature (and on whether the wood is American or European oak), tannins, sweet vanillin, smoky phenols, coconutty oak lactones, and dozens of other similar molecules also leach in. Meanwhile, some of the ethanol oxidizes, eventually yielding ethyl acetate, which imparts a smoother flavor. After a few years, what comes out of those barrels is awfully compelling. American whiskey makers were selling aged booze as early as 1793, and brandy from the French region of Cognac typically spent a year or two in a barrel, too.

But that improvement came at a price. Aging meant losing some of the product to evaporation, through pores in the wooden casks. That loss is called, evocatively, the angels’ share—a portion of spirit offered up to heaven in thanks for a miracle. It’s no small thing: Whiskey makers calculate it at 2 percent a year by volume, which amounts to 18 percent over 10 years. (Of course, that evaporation also concentrates everything left inside, improving flavor.)

This new stage in the manufacturing cycle took the business of spirits to a new level. Now distillers needed real estate to warehouse the casks, and they needed a robust credit economy to fund the manufacture of a product that wouldn’t be sold for years. At the same time, a leisure class had to emerge that would pay a premium to drink something more refined than moonshine.

In other words, the birth of the economic ecosystem surrounding aged liquor represents a signal moment in the early Industrial Revolution, a mile marker on the road to a more civilized world. And somehow that fungus staining the walls of Lakeshore was a byproduct of that journey.

Mycologist James ScottPhoto: Christopher Wahl

When James Scott attended the first day of a mycology course as a freshman in college, his plan was to cut class for the rest of the semester and fake his way through on borrowed notes. But in his lecture that day, the professor told a story about a fungus that lives on peach pits. No one, he said, knows how the fungus gets from one pit to the next. “If you go to an abandoned orchard and lie on your stomach under a tree for a week, watching which insects land on a peach and move to another one,” Scott remembers him saying, “you will know more about this fungus than anyone in the world.”

“It was something even I, an undergraduate who didn’t know anything, could do,” Scott says. “I could go out there and look for stuff.” In the space of one anecdote, Scott had become the sort of person who kept a microscope in his dorm room and decorated the walls with fungal family trees he drew himself. (He also plays the banjo.)

There are between 1.5 million and 5 million species of fungi on earth, and only 100,000 of them have been named according to the (arcane, ancient) rules in the International Code of Botanical Nomenclature. Of those, barely a fifth have gene sequences in GenBank, the world’s main storehouse of genomic data. Only a couple of hundred have been sequenced completely, mostly yeasts with commercial value. Magnified fungi look like a Dr. Seuss illustration rendered by Pixar. It’s a weird landscape, not to everyone’s taste. Among scientists, mycology is not considered a glamour field. “If you found a new deer, you’d be on the cover of Nature,” says John Taylor, a mycologist at UC Berkeley. “If you find a new fungus, you’re in the middle pages of Mycotaxon. But we’re not bitter.”

For hundreds of years, mycologists have named things the old-fashioned way—they’d put a sample under a microscope and describe the shape of its parts, the way it reproduced, the structure of its spores. The rules were typological: To designate a name, a researcher had to have a physical specimen called a type stored in an herbarium somewhere, a description in Latin, and sometimes an illustration of the microscopic structure, too.

That’s all changing now. The genome experts are taking over, planning to hoover up thousands of genetic samples and identify them by their DNA sequences. It’s a controversial shift in a field that has fought wars over nomenclature. Scott, though, was trained in the old school of mycological taxonomy, as practiced by a largely retired generation of scientists who could ID a fungus on sight. “James is a bit of a throwback,” says Keith Seifert, a research scientist with Agriculture and Agri-Food Canada, who has worked with Scott for years. “He’s interested in legacy knowledge.”

“I put maybe a shot of whiskey in a liter of agar and filled the petri plates with it. That made it grow a hell of a lost faster,” Scott says.

In Lakeshore, Scott found the black fungus as far as a mile away from the warehouse. And the closer it was, the thicker it grew, clinging like ashy cotton candy to walls, rooftops, even garden furniture. Under a microscope, it looked to be a mè9lange of different species, but much of it was thick-walled, rough-skinned stuff he’d never seen before. It looked like poorly hewn barrels, strung together end to end. Instantly, Scott realized where the distillery’s other researchers had gone wrong. “They would have taken a sample and scraped it over a petri dish,” Scott says. “And what would have grown were spores that just happened to be passively deposited.” Common fungi were commingled with the mystery stuff in the sample, and the common fungi grew faster. Come back in a couple of weeks and the petri dish would be covered with boring, familiar species—leading to a false conclusion.

Scott had a better way to culture the samples. He ground them up and sprinkled them into a petri dish. But then he put the dish under the microscope and, using an impossibly fine needle, picked out fragments of the rough-skinned fungus and transplanted them to their own dishes. He figured that with no other fungi to compete with, the Lakeshore fungus would flourish.

He waited about a month, came back, and found … not much of anything. Under a microscope the samples were clearly the same black barrel shapes. But his colonies were vanishingly small. Whatever it was, it wasn’t growing like it grew around the warehouse.

Making growth media for fungi is really just feeding them a dish they like to eat. So, on a hunch, Scott bought a bottle of Canadian Club. “I put maybe a shot of whiskey in a liter of agar and filled the petri plates with it,” Scott says. “That made it grow a hell of a lot faster.”

Chances were, Scott thought, it was the ethanol that the spores liked. But how was the fungus getting it in the wild? What connected the ethanol in those aging barrels to the black stuff on the walls of Lakeshore? Scott was still puzzled by this question when, several months later, he told his favorite wine seller about his mystery fungus. The importer, a sommelier-in-training, told him about the angels’ share—and Scott had his connection. The warehouse was venting vaporous ethanol.

A search of the mycology literature for fungi that grew in close proximity to ethanol led Scott to his first guess at what was on the warehouses: the “cellar fungus” Zasmidium cellare, which grows in thick layers inside wine-aging caves. Scott figured the warehouse and its environs were harboring a giant Zasmidium colony. “Based on the similarity of the habitat and the little bit of physical descriptions I could get, I thought that’s what it was,” he says.

Scott ordered a Zasmidium sample from the Centraalbureau voor Schimmelcultures in Utrecht, Netherlands—the world’s most important depot for fungal samples and genomes—and put it under the microscope. It didn’t look anything like the warehouse-staining fungus. Plus, that species grows only in the cool, controlled climate of an aging cave, and whatever was all over Lakeshore grew outside, over a wide temperature range.

He was stumped. All he had was an educated guess that his mystery fungus was part of a group called the “sooty molds.” It happened that an eminent expert on sooty molds, a scientist in his eighties named Stan Hughes, was at Agriculture Canada in Ottawa. And Hughes’ office was down the hall from Canada’s National Herbarium, one of the best collections of fungus specimens in North America. Scott packed his bags.

The mystery fungus.Photo: Caren Alpert

Stan Hughes’ office is on the second floor of a building reminiscent of a 1930s middle school. With his wisps of white hair and a magnifying glass hanging from a silver chain around his neck, he looks every bit the Gandalf of fungi. And perhaps predictably, he is no great fan of modern genetic methods. He was happy to dive into his mothball-scented archive with James “to promote the use of herbarium mycology,” Hughes says, “as opposed to all the chemistry stuff.”

Together, Scott and Hughes rooted around in the herbarium for a couple of days, hitting the literature for possible matches and then diving into the actual samples tucked in their folded-paper envelopes. Eventually, Hughes found a type sample someone had sent the herbarium, a piece of stone roofing tile coated in black fungus. Microscopically and to the naked eye, it was the same stuff that Scott had seen in Lakeshore. It seemed like a match.

But there was a problem: According to the label, the fungus was something called Torula compniacensis, literally “the Torula from Cognac.” Torula is a junk genus, now seen less as a proper taxonomical designation and more as a drawer that old-time researchers threw brownish black fungi into when they didn’t fit anywhere else. It makes mycologists shake their heads like plumbers frowning at a homeowner’s attempt to patch a pipe.

To really understand what this Torula was, Scott knew he’d have to do more than look at it with a microscope. He’d need to trace the literature back to the beginning, too. And what he found was confusing. In 1872, a pharmacist named Antonin Baudoin, director of the agricultural and industrial chemistry laboratory of Cognac, published a pamphlet on a mold blackening the walls around distilleries in Cognac. Baudoin thought, incorrectly, that it was an unnamed member of the algal genus Nostoc and didn’t try to give it a species name. But then Charles Édouard Richon, a mycologist at the French Botanical Society, got wind of Baudoin’s research and took another look. In an 1881 paper, he and a coauthor, citing serious mistakes in Baudoin’s work, reclassified it as the fungus Torula compniacensis. Richon gave some to a colleague, Casimir Roumeguère, who thought it looked like a fungus named earlier by the famous mycologist Pier Andrea Saccardo. Saccardo had gotten the name wrong, and Roumeguère then mistranscribed the incorrect name in an exsiccata, a collectors’ set of fungi samples that enthusiasts circulate to help stabilize nomenclature. Pretty soon there were a bunch of samples of the fungus from Cognac floating around, all mislabeled.

Scott and Hughes traced the error back to its source. “And the herbarium in Ottawa happens to have some of Roumeguè8re’s exsiccati,” Scott says. “So Stan and I were able to go into the herbarium, pull it out, and see exactly what Baudoin had collected.”

Under the microscope, what Richon called Torula compniacensis looked exactly like the samples from Lakeshore. But by a more precise modern definition, this stuff wasn’t Torula. And more work in the herbarium showed that it wasn’t like any other known genus, either. Scott realized he was going to have to name a new branch on the fungal family tree. But he had to follow the rules for nomenclature. “We needed a living culture that we could grow up,” he says. They needed a new sample, an epitype, and it had to come from the same place as the original: France. Scott prevailed on a colleague to detour to Cognac after a Paris conference; he sent back a few fungus-covered twigs from a bush outside the gift shop at cognac-maker Rémy Martin. It was a perfect match to the Richon specimen from 1881.

The discovery of a new fungal species might not make much noise, but a new genus—the next taxonomic category up the tree—is pretty cool. Scott and his colleagues nervously set about coming up with a brand-new name. He couldn’t name it after himself; that’s unspeakably crass in the fungal world. And Hughes already had dozens of species and genuses named after him. So the team settled on honoring the man who first brought the stuff to the attention of mycologists. They named the new genus Baudoinia, and they left the species name alone: compniacensis. In other words: Baudoin’s fungus from Cognac.

Just because the fungus now had a name didn’t mean the folks at Hiram Walker suddenly knew how to keep it from growing on their neighbors’ walls. As Scott was doing his research, transnational liquor conglomerate Pernod-Ricard purchased the Hiram Walker distillery, and the last thing the company wanted to hear was that fumes from its warehouse were making mold grow on nearby homes. Better to pay into a fund for powerwashing the neighborhood once a year and be done with it. That seemed to satisfy the Ontario Ministry of the Environment, so it was good enough for Pernod Ricard. When Scott’s contract ran out in September 2009, he and the company parted ways.

But by then, Scott had become obsessed with discovering how Baudoinia worked. After all, his name is next to it in the books. How did the mold use the angels’ share? A genetic analysis showed that it was only distantly related to cellar fungus, and researchers at a Department of Energy genomics lab—always looking for potential new ways to turn plants into ethanol for biofuel—added Baudoinia to their list of fungi-to-do. Physiological studies suggested that the ethanol helps the fungus produce heat-shock proteins, protective against temperature extremes, which might explain how it can survive the wide range of temperatures in habitats from Cognac to Canada to Kentucky.

Even weirder, how does a fungus that’s millions of years old, older than Homo sapiens, find a near-perfect ecological niche amid stuff people have been making for only a couple of centuries? Presumably somewhere in the world, naturally occurring Baudoinia lives adjacent to naturally fermenting fruit—or maybe it’s everywhere, a sluggish loser until it gets a whiff of ethanol. Evolution is full of stories of animals and plants fitting into hyper-specific man-made niches, as if nature somehow got the specs in advance. “It’s an urban extremophile,” Scott says. Typically we don’t think of cities as being particularly extreme environments, but few places on earth get as hot as a rooftop or as dry as the corner of a heated living room. Fungi live in both. Now Scott sees urban extremophile fungi everywhere. The black smudges along roadsides and on old buildings that look like soot, he says, are usually some hardy fungus that tolerates (or loves) diesel fumes, smog, and slightly acidic rain. Baudoinia might have been a bit player on prehuman Earth. But then we came along and built distilleries, Baudoinia‘s own bespoke microparadises.

Today, Scott is a tenured professor at the University of Toronto. Sporometrics has flourished since he took that first phone call a decade ago. The offices are now in a former industrial neighborhood of Toronto given over to new media companies and architecture ateliers, but Baudoinia experiments are still ongoing in the tidy, small laboratory in back. And Scott is still collecting samples. In fact, one snowy day he drove about 100 miles north of Toronto to Collingwood, on the southern tip of Lake Huron’s Georgian Bay, to yet another distillery, chasing Baudoinia. On Google Earth he’d seen black stuff all over the walls of the home of Canadian Mist.

Just as in Lakeshore, the air in Collingwood was redolent of whiskey. The walls, street signs, and trees were coated in mold, up to an eighth of an inch thick in some places. Scott snipped a branch off a blackened, bare tree, threw it into the back seat of his Nissan SUV, and drove back to Toronto.

But under the microscope at Sporometrics, the sample didn’t look anything like Baudoinia. “No way,” Scott says, sitting cross-legged in his chair and looking at the flatscreen hooked up to the scope. “What’s all this?” He points at tiny clear spores dotting the brownish-black mass of fungus. “It’s got these round, rough things, and these smooth hyphae,” he says, referring to the branching filaments that characterize fungi. He rests his chin in his hands. He looks stumped. Then he straightens up. “No. That’s great. It makes it even cooler,” he says, beginning to smile. Maybe he’ll spend tonight making up some agar to see what grows.